diff --git a/pkg/index/index.go b/pkg/index/index.go
index 54bc84c19..b651c317b 100644
--- a/pkg/index/index.go
+++ b/pkg/index/index.go
@@ -49,8 +49,8 @@ func init() {
 
 type Index struct {
 	*blobserver.NoImplStorage
-
-	s sorted.KeyValue
+	reindex bool // whether "reindex" was set in config (likely via perkeepd flag)
+	s       sorted.KeyValue
 
 	KeyFetcher blob.Fetcher // for verifying claims
 
@@ -389,6 +389,7 @@ func newFromConfig(ld blobserver.Loader, config jsonconfig.Obj) (blobserver.Stor
 		}
 		ix, err = New(kv)
 	}
+	ix.reindex = reindex
 	if reindex {
 		ix.hasWiped = true
 	}
@@ -441,6 +442,8 @@ func ReindexMaxProcs() int {
 	return reindexMaxProcs.v
 }
 
+func (x *Index) WantsReindex() bool { return x.reindex }
+
 func (x *Index) Reindex() error {
 	x.Lock()
 	if x.blobSource == nil {
diff --git a/pkg/serverinit/serverinit.go b/pkg/serverinit/serverinit.go
index bbf001c92..f5312778d 100644
--- a/pkg/serverinit/serverinit.go
+++ b/pkg/serverinit/serverinit.go
@@ -68,6 +68,7 @@ type handlerConfig struct {
 	settingUp, setupDone bool
 }
 
+// handlerLoader implements blobserver.Loader.
 type handlerLoader struct {
 	installer   HandlerInstaller
 	baseURL     string
@@ -76,9 +77,10 @@ type handlerLoader struct {
 	curPrefix   string
 	closers     []io.Closer
 	prefixStack []string
-	reindex     bool
 }
 
+var _ blobserver.Loader = (*handlerLoader)(nil)
+
 // A HandlerInstaller is anything that can register an HTTP Handler at
 // a prefix path.  Both *http.ServeMux and perkeep.org/pkg/webserver.Server
 // implement HandlerInstaller.
@@ -307,18 +309,14 @@ func (hl *handlerLoader) setupHandler(prefix string) {
 	hl.curPrefix = prefix
 
 	if strings.HasPrefix(h.htype, "storage-") {
-		// Assume a storage interface
+		// Assume a storage interface:
 		stype := strings.TrimPrefix(h.htype, "storage-")
-		if h.htype == "storage-index" && hl.reindex {
-			// Let the indexer know that we're in reindex mode
-			h.conf["reindex"] = true
-		}
 		pstorage, err := blobserver.CreateStorage(stype, hl, h.conf)
 		if err != nil {
 			exitFailure("error instantiating storage for prefix %q, type %q: %v",
 				h.prefix, stype, err)
 		}
-		if ix, ok := pstorage.(*index.Index); ok && hl.reindex {
+		if ix, ok := pstorage.(*index.Index); ok && ix.WantsReindex() {
 			log.Printf("Reindexing %s ...", h.prefix)
 			if err := ix.Reindex(); err != nil {
 				exitFailure("Error reindexing %s: %v", h.prefix, err)
@@ -588,6 +586,28 @@ func (c *Config) checkValidAuth() error {
 	return err
 }
 
+func (c *Config) SetReindex(v bool) {
+	prefixes, _ := c.jconf["prefixes"].(map[string]interface{})
+	for prefix, vei := range prefixes {
+		if prefix == "_knownkeys" {
+			continue
+		}
+		pmap, ok := vei.(map[string]interface{})
+		if !ok {
+			continue
+		}
+		pconf := jsonconfig.Obj(pmap)
+		typ, _ := pconf["handler"].(string)
+		if typ != "storage-index" {
+			continue
+		}
+		opts, ok := pconf["handlerArgs"].(map[string]interface{})
+		if ok {
+			opts["reindex"] = v
+		}
+	}
+}
+
 // InstallHandlers creates and registers all the HTTP Handlers needed
 // by config into the provided HandlerInstaller and validates that the
 // configuration is valid.
@@ -596,7 +616,7 @@ func (c *Config) checkValidAuth() error {
 //
 // The returned shutdown value can be used to cleanly shut down the
 // handlers.
-func (c *Config) InstallHandlers(hi HandlerInstaller, baseURL string, reindex bool) (shutdown io.Closer, err error) {
+func (c *Config) InstallHandlers(hi HandlerInstaller, baseURL string) (shutdown io.Closer, err error) {
 	config := c
 	defer func() {
 		if e := recover(); e != nil {
@@ -629,7 +649,6 @@ func (c *Config) InstallHandlers(hi HandlerInstaller, baseURL string, reindex bo
 		baseURL:   baseURL,
 		config:    make(map[string]*handlerConfig),
 		handler:   make(map[string]interface{}),
-		reindex:   reindex,
 	}
 
 	for prefix, vei := range prefixes {
diff --git a/server/perkeepd/perkeepd.go b/server/perkeepd/perkeepd.go
index efb070b04..33d69982a 100644
--- a/server/perkeepd/perkeepd.go
+++ b/server/perkeepd/perkeepd.go
@@ -434,8 +434,10 @@ func Main() {
 		exitf("Error registering challenge client with Perkeep muxer: %v", err)
 	}
 
+	config.SetReindex(*flagReindex)
+
 	// Finally, install the handlers. This also does the final config validation.
-	shutdownCloser, err := config.InstallHandlers(ws, baseURL, *flagReindex)
+	shutdownCloser, err := config.InstallHandlers(ws, baseURL)
 	if err != nil {
 		exitf("Error parsing config: %v", err)
 	}